I guess why we didn't see difference in kinetic energy is prabobaly
because the energy was being synchronized in TI simulation. However,
the temprature in output used the synchronized energy, but different
degrees of freedom, thus we saw different temparture in two output. So
I think it's parabobaly worth a while to making sure we have correct
degrees of freedom in such simulations.
What I am doing is, whenever the QM/MM boundary cross a QM-MM(H)
hydrogen bond (and when qmshake=0, i.e. no shake applied to the QM
region), we remove all the connectivities between the H atom and other
bonded QM atoms, making it a free particle.
Best,
Qiantao
On Sat, Sep 24, 2011 at 8:51 AM, case <case.biomaps.rutgers.edu> wrote:
> On Fri, Sep 23, 2011, Brian Radak wrote:
>>
>> Does this difference in degrees of freedom have any bearing on the dynamics
>> or is it just a quirk of the output?
>
> I would have thought that the thermostat would have been affected, and hence
> the velocities on two sides. But if that happened, the kinetic energies would
> not be equal, and very quickly the coordinates and potential energies would
> not match. Since that is not happening, it looks like just a quirk in the
> output.
>
> I must say that having an O-H bond cross the QM/MM boundary sounds very odd.
> We certainly never looked at anything like this when developing or testing the
> code. Let's see how Qiantao's fix works out.
>
> ...dac
>
>
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Received on Sun Sep 25 2011 - 06:30:02 PDT
